On 8/08/2012 5:58 PM, Du Jiangfeng (BIOCH) wrote:
Dear All,
I encountered a very weird result after performing NVT simulation, all the
waters aligned in lines, and they look like crystal cells.
If they're in geometric lines, then you're probably looking at your
input configuration. If they're just close to being in lines, you've
probably used position restraints on them. Compare how they look with
other Martini simulations, e.g. from tutorials.
Mark
How did it turn out like this by temperature coupling? The following is the
nvt.mdp parameters:
; NVT equilibration
define = -DPOSRES ; position restrain the protein but free the
waters and lipids
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 120000 ; 0.025 * 120000 = 3 ns
dt = 0.025 ; 25 fs since this is coarse grained system
with martini force field
; Output control
nstxout = 100 ; save coordinates every 2.5 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = yes ; first dynamics run
constraint_algorithm = LINCS ; holonomic constraints
constraints = none ; I suppose "none" is standard used in martini force
field
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
lincs_warnangle = 30
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 250 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.2 0.2 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in
K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Which parameters should be blamed to cause such artificial result?
Thank you!
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands--
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